Is the scanner not working with the built-in USB redirection? I seem to recall Microsoft making a big deal about this feature when 2008 R2 was released. I know that not all devices work perfectly with it, but I haven't seen many that didn't.
The only other option that I've tried is using Quest vWorkspace, which is probably way overkill for what you need. It's really more of a unified Terminal Services and VDI solution, i.e., it includes its own RDP client, connection broker, and proprietary RDP protocol that is optimized for multimedia and better USB compatibility. I worked with one client who had tried nearly every solution out there to get their USB fingerprint scanners to work via RDP and USB redirection, and vWorkspace was the only thing (at the time) that had them working correctly.
________________________________________
CompTIA A+, Network+, Server+, Security+
MCTS:Windows 7
MCSE:Security 2003
MCITP:Server Administrator
MCITP:Enterprise Administrator
MCITP:Virtualization Administrator 2008 R2
Certified Quest vWorkspace Administrator